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  1. Understanding gene transcription and mRNA-protein (mRNP) dynamics in single cells in a multicellular organism has been challenging. The catalytically dead CRISPR-Cas13 (dCas13) system has been used to visualiz...

    Authors: Youkui Huang, Bao-Qing Gao, Quan Meng, Liang-Zhong Yang, Xu-Kai Ma, Hao Wu, Yu-Hang Pan, Li Yang, Dong Li and Ling-Ling Chen
    Citation: Genome Biology 2023 24:15
  2. High-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported.

    Authors: Lingbin Ni, Yucheng Liu, Xin Ma, Tengfei Liu, Xiaoyue Yang, Zhao Wang, Qianjin Liang, Shulin Liu, Min Zhang, Zheng Wang, Yanting Shen and Zhixi Tian
    Citation: Genome Biology 2023 24:12
  3. Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficu...

    Authors: Divyaratan Popli, Stéphane Peyrégne and Benjamin M. Peter
    Citation: Genome Biology 2023 24:10
  4. CRISPR-Cas13 is a newly emerging RNA knockdown technology that is comparable to RNAi. Among all members of Cas13, CasRx degrades RNA in human cells with high precision and effectiveness. However, it remains un...

    Authors: Yonghao Zhan, Congcong Cao, Aolin Li, Hongbing Mei and Yuchen Liu
    Citation: Genome Biology 2023 24:9
  5. CRISPR-based toolkits have dramatically increased the ease of genome and epigenome editing. SpCas9 is the most widely used nuclease. However, the difficulty of delivering SpCas9 and inability to modulate its e...

    Authors: Qin Jin, Xiaoyi Liu, Zhenpeng Zhuang, Jiayuan Huang, Shixue Gou, Hui Shi, Yu Zhao, Zhen Ouyang, Zhaoming Liu, Lei Li, Junjie Mao, Weikai Ge, Fangbing Chen, Manya Yu, Yezhi Guan, Yinghua Ye…
    Citation: Genome Biology 2023 24:8
  6. Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain ...

    Authors: Long Zhao, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, Xiaomin Bie, Jiafu Jiang, Xiaoqi Feng, Xiangdong Fu, Xiansheng Zhang, Zhuo Du and Jun Xiao
    Citation: Genome Biology 2023 24:7
  7. Testing an ever-increasing number of CRISPR components is challenging when developing new genome engineering tools. Plant biotechnology has few high-throughput options to perform iterative design-build-test-le...

    Authors: Christophe Gaillochet, Alexandra Peña Fernández, Vera Goossens, Katelijn D’Halluin, Andrzej Drozdzecki, Myriam Shafie, Julie Van Duyse, Gert Van Isterdael, Camila Gonzalez, Mattias Vermeersch, Jonas De Saeger, Ward Develtere, Dominique Audenaert, David De Vleesschauwer, Frank Meulewaeter and Thomas B. Jacobs
    Citation: Genome Biology 2023 24:6
  8. Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL at human genomic r...

    Authors: Chathura J. Gunasekara, Harry MacKay, C. Anthony Scott, Shaobo Li, Eleonora Laritsky, Maria S. Baker, Sandra L. Grimm, Goo Jun, Yumei Li, Rui Chen, Joseph L. Wiemels, Cristian Coarfa and Robert A. Waterland
    Citation: Genome Biology 2023 24:2
  9. Secure multiparty computation (MPC) is a cryptographic tool that allows computation on top of sensitive biomedical data without revealing private information to the involved entities. Here, we introduce Sequre...

    Authors: Haris Smajlović, Ariya Shajii, Bonnie Berger, Hyunghoon Cho and Ibrahim Numanagić
    Citation: Genome Biology 2023 24:5
  10. We present a novel genome-wide off-target prediction method named Extru-seq and compare it with cell-based (GUIDE-seq), in vitro (Digenome-seq), and in silico methods using promiscuous guide RNAs with large nu...

    Authors: Jeonghun Kwon, Minyoung Kim, Woochang Hwang, Anna Jo, Gue-Ho Hwang, Minhee Jung, Un Gi Kim, Gang Cui, Heonseok Kim, Joon-Ho Eom, Junho K. Hur, Junwon Lee, Youngho Kim, Jin-soo Kim, Sangsu Bae and Jungjoon K. Lee
    Citation: Genome Biology 2023 24:4
  11. Xylem, the most abundant tissue on Earth, is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells. In most angiospe...

    Authors: Chia-Chun Tung, Shang-Che Kuo, Chia-Ling Yang, Jhong-He Yu, Chia-En Huang, Pin-Chien Liou, Ying-Hsuan Sun, Peng Shuai, Jung-Chen Su, Chuan Ku and Ying-Chung Jimmy Lin
    Citation: Genome Biology 2023 24:3
  12. Binning aims to recover microbial genomes from metagenomic data. For complex metagenomic communities, the available binning methods are far from satisfactory, which usually do not fully use different types of ...

    Authors: Ziye Wang, Pingqin Huang, Ronghui You, Fengzhu Sun and Shanfeng Zhu
    Citation: Genome Biology 2023 24:1
  13. The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common approaches for comparing SVs were developed alongsid...

    Authors: Adam C. English, Vipin K. Menon, Richard A. Gibbs, Ginger A. Metcalf and Fritz J. Sedlazeck
    Citation: Genome Biology 2022 23:271
  14. A major question in systems biology is how to identify the core gene regulatory circuit that governs the decision-making of a biological process. Here, we develop a computational platform, named NetAct, for co...

    Authors: Kenong Su, Ataur Katebi, Vivek Kohar, Benjamin Clauss, Danya Gordin, Zhaohui S. Qin, R. Krishna M. Karuturi, Sheng Li and Mingyang Lu
    Citation: Genome Biology 2022 23:270
  15. Most single-cell RNA sequencing (scRNA-seq) analyses begin with cell clustering; thus, the clustering accuracy considerably impacts the validity of downstream analyses. In contrast with the abundance of cluste...

    Authors: Jiyuan Fang, Cliburn Chan, Kouros Owzar, Liuyang Wang, Diyuan Qin, Qi-Jing Li and Jichun Xie
    Citation: Genome Biology 2022 23:269
  16. Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understandi...

    Authors: Stavroula Kanoni, Sarah E. Graham, Yuxuan Wang, Ida Surakka, Shweta Ramdas, Xiang Zhu, Shoa L. Clarke, Konain Fatima Bhatti, Sailaja Vedantam, Thomas W. Winkler, Adam E. Locke, Eirini Marouli, Greg J. M. Zajac, Kuan-Han H. Wu, Ioanna Ntalla, Qin Hui…
    Citation: Genome Biology 2022 23:268
  17. Quality control (QC) of cells, a critical first step in single-cell RNA sequencing data analysis, has largely relied on arbitrarily fixed data-agnostic thresholds applied to QC metrics such as gene complexity ...

    Authors: Ayshwarya Subramanian, Mikhail Alperovich, Yiming Yang and Bo Li
    Citation: Genome Biology 2022 23:267
  18. Lynch syndrome (LS) is a cancer predisposition syndrome affecting more than 1 in every 300 individuals worldwide. Clinical genetic testing for LS can be life-saving but is complicated by the heavy burden of va...

    Authors: Anthony Scott, Felicia Hernandez, Adam Chamberlin, Cathy Smith, Rachid Karam and Jacob O. Kitzman
    Citation: Genome Biology 2022 23:266
  19. The tumor microenvironment (TME) has been shown to strongly influence treatment outcome for cancer patients in various indications and to influence the overall survival. However, the cells forming the TME in g...

    Authors: Boxi Kang, Jordi Camps, Biao Fan, Hongpeng Jiang, Mahmoud M. Ibrahim, Xueda Hu, Shishang Qin, Dennis Kirchhoff, Derek Y. Chiang, Shan Wang, Yingjiang Ye, Zhanlong Shen, Zhaode Bu, Zemin Zhang and Helge G. Roider
    Citation: Genome Biology 2022 23:265
  20. Heterosis is widely used in agriculture. However, its molecular mechanisms are still unclear in plants. Here, we develop, sequence, and record the phenotypes of 418 hybrids from crosses between two testers and...

    Authors: Jianyin Xie, Weiping Wang, Tao Yang, Quan Zhang, Zhifang Zhang, Xiaoyang Zhu, Ni Li, Linran Zhi, Xiaoqian Ma, Shuyang Zhang, Yan Liu, Xueqiang Wang, Fengmei Li, Yan Zhao, Xuewei Jia, Jieyu Zhou…
    Citation: Genome Biology 2022 23:264
  21. Despite its conserved role on gene expression and transposable element (TE) silencing, genome-wide CG methylation differs substantially between wild Arabidopsis thaliana accessions.

    Authors: Thanvi Srikant, Wei Yuan, Kenneth Wayne Berendzen, Adrián Contreras-Garrido, Hajk-Georg Drost, Rebecca Schwab and Detlef Weigel
    Citation: Genome Biology 2022 23:263
  22. Chinese cabbage (Brassica rapa ssp. pekinensis) experienced a whole-genome triplication event and thus has three subgenomes: least fractioned, medium fractioned, and most fractioned subgenome. Environmental ch...

    Authors: Xiaoxue Sun, Daling Feng, Mengyang Liu, Ruixin Qin, Yan Li, Yin Lu, Xiaomeng Zhang, Yanhua Wang, Shuxing Shen, Wei Ma and Jianjun Zhao
    Citation: Genome Biology 2022 23:262
  23. Many biological processes, such as cell division cycle and drug resistance, are reflected in protein covariation across single cells. This covariation can be quantified and interpreted by single-cell mass spec...

    Authors: Andrew Leduc, R. Gray Huffman, Joshua Cantlon, Saad Khan and Nikolai Slavov
    Citation: Genome Biology 2022 23:261
  24. G-quadruplexes (G4s) are unique noncanonical nucleic acid secondary structures, which have been proposed to physically interact with transcription factors and chromatin remodelers to regulate cell type-specifi...

    Authors: Conghui Li, Zhinang Yin, Ruijing Xiao, Beili Huang, Yali Cui, Honghong Wang, Ying Xiang, Lingrui Wang, Lingyu Lei, Jiaqin Ye, Tianyu Li, Youquan Zhong, Fangteng Guo, Yuchen Xia, Pingping Fang and Kaiwei Liang
    Citation: Genome Biology 2022 23:259
  25. Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and patching, and we ...

    Authors: Michael Alonge, Ludivine Lebeigle, Melanie Kirsche, Katie Jenike, Shujun Ou, Sergey Aganezov, Xingang Wang, Zachary B. Lippman, Michael C. Schatz and Sebastian Soyk
    Citation: Genome Biology 2022 23:258
  26. Expansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is part...

    Authors: Harriet Dashnow, Brent S. Pedersen, Laurel Hiatt, Joe Brown, Sarah J. Beecroft, Gianina Ravenscroft, Amy J. LaCroix, Phillipa Lamont, Richard H. Roxburgh, Miriam J. Rodrigues, Mark Davis, Heather C. Mefford, Nigel G. Laing and Aaron R. Quinlan
    Citation: Genome Biology 2022 23:257
  27. Spatial omics technologies enable a deeper understanding of cellular organizations and interactions within a tissue of interest. These assays can identify specific compartments or regions in a tissue with diff...

    Authors: Jiwoon Park, Junbum Kim, Tyler Lewy, Charles M. Rice, Olivier Elemento, André F. Rendeiro and Christopher E. Mason
    Citation: Genome Biology 2022 23:256
  28. The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant ...

    Authors: Keyur Talsania, Tsai-wei Shen, Xiongfong Chen, Erich Jaeger, Zhipan Li, Zhong Chen, Wanqiu Chen, Bao Tran, Rebecca Kusko, Limin Wang, Andy Wing Chun Pang, Zhaowei Yang, Sulbha Choudhari, Michael Colgan, Li Tai Fang, Andrew Carroll…
    Citation: Genome Biology 2022 23:255
  29. The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim “Mittelhofen,” in present-day Germany, dat...

    Authors: Joanna H. Bonczarowska, Julian Susat, Barbara Mühlemann, Isabelle Jasch-Boley, Sebastian Brather, Benjamin Höke, Susanne Brather-Walter, Valerie Schoenenberg, Jonathan Scheschkewitz, Gabriele Graenert, Dirk Krausse, Michael Francken, Terry C. Jones, Joachim Wahl, Almut Nebel and Ben Krause-Kyora
    Citation: Genome Biology 2022 23:250
  30. Eukaryotic ribosomes are widely presumed to scan mRNA for the AUG codon to initiate translation in a strictly 5′–3′ movement (i.e., strictly unidirectional scanning model), so that ribosomes initiate translati...

    Authors: Ke Li, Jinhui Kong, Shuo Zhang, Tong Zhao and Wenfeng Qian
    Citation: Genome Biology 2022 23:254
  31. JUNB transcription factor contributes to the formation of the ubiquitous transcriptional complex AP-1 involved in the control of many physiological and disease-associated functions. The roles of JUNB in the co...

    Authors: Beatriz Pérez-Benavente, Alihamze Fathinajafabadi, Lorena de la Fuente, Carolina Gandía, Arantxa Martínez-Férriz, José Miguel Pardo-Sánchez, Lara Milián, Ana Conesa, Octavio A. Romero, Julián Carretero, Rune Matthiesen, Isabelle Jariel-Encontre, Marc Piechaczyk and Rosa Farràs
    Citation: Genome Biology 2022 23:252
  32. Despite having been extensively studied, it remains largely unclear why humans bear a particularly high risk of cancer. The antagonistic pleiotropy hypothesis predicts that primate-specific genes (PSGs) tend t...

    Authors: Chenyu Ma, Chunyan Li, Huijing Ma, Daqi Yu, Yufei Zhang, Dan Zhang, Tianhan Su, Jianmin Wu, Xiaoyue Wang, Li Zhang, Chun-Long Chen and Yong E. Zhang
    Citation: Genome Biology 2022 23:251
  33. DNA N6-methyldeoxyadenosine (6mA) is rarely present in mammalian cells and its nuclear role remains elusive.

    Authors: Kai-Wen Hsu, Joseph Chieh-Yu Lai, Jeng-Shou Chang, Pei-Hua Peng, Ching-Hui Huang, Der-Yen Lee, Yu-Cheng Tsai, Chi-Jung Chung, Han Chang, Chao-Hsiang Chang, Ji-Lin Chen, See-Tong Pang, Ziyang Hao, Xiao-Long Cui, Chuan He and Kou-Juey Wu
    Citation: Genome Biology 2022 23:249
  34. We present SIEVE, a statistical method for the joint inference of somatic variants and cell phylogeny under the finite-sites assumption from single-cell DNA sequencing. SIEVE leverages raw read counts for all ...

    Authors: Senbai Kang, Nico Borgsmüller, Monica Valecha, Jack Kuipers, Joao M. Alves, Sonia Prado-López, Débora Chantada, Niko Beerenwinkel, David Posada and Ewa Szczurek
    Citation: Genome Biology 2022 23:248
  35. DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capa...

    Authors: Roberto Rossini, Vipin Kumar, Anthony Mathelier, Torbjørn Rognes and Jonas Paulsen
    Citation: Genome Biology 2022 23:247
  36. Mammalian cells have three types of RNA polymerases (Pols), Pol I, II, and III. However, the extent to which these polymerases are cross-regulated and the underlying mechanisms remain unclear.

    Authors: Yongpeng Jiang, Jie Huang, Kai Tian, Xiao Yi, Haonan Zheng, Yi Zhu, Tiannan Guo and Xiong Ji
    Citation: Genome Biology 2022 23:246
  37. Heat-imposed crop failure is often attributed to reduced thermotolerance of floral tissues; however, the underlying mechanism remains unknown. Here, we demonstrate that m6A RNA methylation increases in Arabidopsi...

    Authors: Ling Wang, Haiyan Zhuang, Wenwen Fan, Xia Zhang, Haihong Dong, Hongxing Yang and Jungnam Cho
    Citation: Genome Biology 2022 23:244
  38. Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-genom...

    Authors: Marina Brasó-Vives, Ferdinand Marlétaz, Amina Echchiki, Federica Mantica, Rafael D. Acemel, José L. Gómez-Skarmeta, Diego A. Hartasánchez, Lorlane Le Targa, Pierre Pontarotti, Juan J. Tena, Ignacio Maeso, Hector Escriva, Manuel Irimia and Marc Robinson-Rechavi
    Citation: Genome Biology 2022 23:243
  39. Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. ...

    Authors: Tom L. Kaufmann, Marina Petkovic, Thomas B. K. Watkins, Emma C. Colliver, Sofya Laskina, Nisha Thapa, Darlan C. Minussi, Nicholas Navin, Charles Swanton, Peter Van Loo, Kerstin Haase, Maxime Tarabichi and Roland F. Schwarz
    Citation: Genome Biology 2022 23:241
  40. There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but relia...

    Authors: Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson and Abhinav Nellore
    Citation: Genome Biology 2022 23:240
  41. The use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a reference for detecting the full spectrum of somatic events from cancers has long been ad...

    Authors: Chunlin Xiao, Zhong Chen, Wanqiu Chen, Cory Padilla, Michael Colgan, Wenjun Wu, Li-Tai Fang, Tiantian Liu, Yibin Yang, Valerie Schneider, Charles Wang and Wenming Xiao
    Citation: Genome Biology 2022 23:237
  42. Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that ...

    Authors: Jasmijn A. Baaijens, Alessandro Zulli, Isabel M. Ott, Ioanna Nika, Mart J. van der Lugt, Mary E. Petrone, Tara Alpert, Joseph R. Fauver, Chaney C. Kalinich, Chantal B. F. Vogels, Mallery I. Breban, Claire Duvallet, Kyle A. McElroy, Newsha Ghaeli, Maxim Imakaev, Malaika F. Mckenzie-Bennett…
    Citation: Genome Biology 2022 23:236

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